Jōnin (上忍, High Ninja) are generally highly-experienced shinobi with great individual skill who serve as military captains. They are often sent on A-rank missions, and experienced jōnin may even be sent on S-rank missions (which are considered to be the greatest difficulty). It is not unusual for jōnin to go on missions alone. Jōnin are generally able to use at least two types of elemental chakra, some genjutsu, and above average taijutsu skills.

The ways to achieve this rank are unique for each village, its depends on the rules. In Five Great Nations, the way to gain the title is passing the examination with their Kage and other elders as judges. In Amegakure, the requirement is quite similar to the Five Great Nations except that the judges are the leader and some high ranked shinobi. When a ninja becomes a jōnin, they may be assigned a three-man genin team to supervise. One part of their duties is to help instruct and train these genin to become competent ninja. In Konohagakure, it is up to the jōnin to decide whether a candidate Hokage would be given the position permanently. They also have a special rank known as Jōnin Commander. Shinobi who have jōnin-level skills only in a specialised area are classified as Tokubetsu Jōnin.